Temperature-dependent hydrogen-bond geometry in liquid water

Pressure-induced hydrogen bonding modulating Fermi resonance between fundamental modes in xylitol molecule

Xylitol, as a typical polyol, has a broad range of application prospects. However, the molecular states of xylitol under different environments are rarely reported until now. In this work, the state changes of xylitol molecules under high pressure were analyzed by Raman spectra. A Fermi resonance phenomenon in the fundamental mode of xylitol at 2945 (±0.06) cm-1 and 2955 (±0.41) cm-1 was observed at 0.99 GPa. The Fermi doublets possess the same symmetry and close energy levels, which had not been changed by pressures. However, the high pressure shortened the atomic distances and applied the extra disturbance, providing the necessary conditions for energy transfer. Besides, the Fermi doublets decoupling happened at 4 GPa due to the breaking of hydrogen bonding. This work provides an important reference for studying molecular states and weak interactions of polyols under high pressures.

TMAO perturbs intermolecular vibrational motions of water revealed by low-frequency modes

Trimethylamine N-oxide (TMAO) as a representative natural osmolyte has received much attention because of its unique properties, including enhancement of hydrogen bonding networks in liquid water and stabilization of three-dimensional structures of proteins in living organisms. As a hydrogen bond maker and/or a protein stabilizer, its hydrated structures and orientation dynamics in aqueous solutions have been investigated by various spectroscopic methods. Particularly, distinct from other natural osmolytes, it has been found that TMAO molecules form complexes with water molecules even at low concentrations, showing extraordinarily long lifetimes and much larger effective dipole moments. In this study, we demonstrated that collective motions of water molecules are closely correlated to TMAO molecules, as revealed by the changes of the librational modes observed in hyper-Raman (HR) spectra in the low-frequency region (<1000 cm-1) for the first time. Based on HR spectra of the TMAO solutions at submolar concentrations, we observed that the librational bands originating from water apparently upshift (∼15 cm-1) upon the addition of TMAO molecules. Compared to the OH stretching band of water showing a negligible downshift (<5 cm-1), the librational bands of water are more sensitive to reflect changes in the hydrogen bonding networks in the TMAO solutions, suggesting formation of transient TMAO-water complexes plays an essential role toward surrounding water molecules in perturbing their librational motions. We expect to provide a supplementary approach to understand that water molecules in TMAO aqueous solutions are strongly affected by TMAO molecules, different from other osmolytes.

Second inflection point of supercooled water surface tension induced by hydrogen bonds: A molecular-dynamics study

Surface tension of supercooled water is a fundamental property in various scientific processes. In this study, we perform molecular dynamics simulations with the TIP4P-2005 model to investigate the surface tension of supercooled water down to 220 K. Our results show a second inflection point (SIP) in the surface tension at temperature TSIP ≈ 267.5 ± 2.3 K. Using an extended IAPWS-E functional fit for the water surface tension, we calculate the surface excess internal-energy and entropy terms of the excess Helmholtz free energy. Similar to prior studies [Wang et al., Phys. Chem. Chem. Phys. 21, 3360 (2019); Gorfer et al., J. Chem. Phys. 158, 054503 (2023)], our results show that the surface tension is governed by two driving forces: a surface excess entropy change above the SIP and a surface excess internal-energy change below it. We study hydrogen-bonding near the SIP because it is the main cause of water's anomalous properties. With decreasing temperature, our results show that the entropy contribution to the surface tension reaches a maximum slightly below the SIP and then decreases. This is because the number of hydrogen bonds increases more slowly below the SIP. Moreover, the strengths and lifetimes of the hydrogen bonds also rise dramatically below the SIP, causing the internal-energy term to dominate the excess surface free energy. Thus, the SIP in the surface tension of supercooled TIP4P-2005 water is associated with an increase in the strengths and lifetimes of hydrogen bonds, along with a decrease in the formation rate (#/K) of new hydrogen bonds.

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.

Evaluation of Viscosity Changes and Rheological Properties of Diutan Gum, Xanthan Gum, and Scleroglucan in Extreme Reservoirs

The chemically synthesized polymer polyacrylamide (HPAM) has achieved excellent oil displacement in conventional reservoirs, but its oil displacement is poor in extreme reservoir environments. To develop a biopolymer oil flooding agent suitable for extreme reservoir conditions, the viscosity changes and rheological properties of three biopolymers, diutan gum, xanthan gum, and scleroglucan, were studied under extreme reservoir conditions (high salt, high temperature, strong acid, and alkali), and the effects of temperature, mineralization, pH, and other factors on their viscosities and long-term stability were analyzed and compared. The results show that the three biopolymers had the best viscosity-increasing ability at temperatures of 90 °C and below. The viscosity of the three biopolymers was 80.94 mPa·s, 11.57 mPa·s, and 59.83 mPa·s, respectively, when the concentration was 1500 mg/L and the salinity 220 g/L. At the shear rate of 250 s-1, 100 °C~140 °C, scleroglucan had the best viscosification. At 140 °C, the solution viscosity was 19.74 mPa·s, and the retention rate could reach 118.27%. The results of the long-term stability study showed that the solution viscosity of scleroglucan with a mineralization level of 220 mg/L was 89.54% viscosity retention in 40 days, and the diutan gum could be stabilized for 10 days, with the viscosity maintained at 90 mPa·s. All three biopolymers were highly acid- and alkali-resistant, with viscosity variations of less than 15% in the pH3~10 range. Rheological tests showed that the unique double-helix structure of diutan gum and the rigid triple-helix structure of scleroglucan caused them to have better viscoelastic properties than xanthan gum. Therefore, these two biopolymers, diutan gum, and scleroglucan, have the potential for extreme reservoir oil displacement applications. It is recommended to use diutan gum for oil displacement in reservoirs up to 90 °C and scleroglucan for oil displacement in reservoirs between 100 °C and 140 °C.

Imaging temperature and thickness of thin planar liquid water jets in vacuum

We present spatially resolved measurements of the temperature of a flat liquid water microjet for varying ambient pressures, from vacuum to 100% relative humidity. The entire jet surface is probed in a single shot by a high-resolution infrared camera. Obtained 2D images are substantially influenced by the temperature of the apparatus on the opposite side of the infrared camera; a protocol to correct for the thermal background radiation is presented. In vacuum, we observe cooling rates due to water evaporation on the order of 10⁵ K/s. For our system, this corresponds to a temperature decrease in approximately 15 K between upstream and downstream positions of the flowing leaf. Making reasonable assumptions on the absorption of the thermal background radiation in the flatjet, we can extend our analysis to infer a thickness map. For a reference system, our value for the thickness is in good agreement with the one reported from white light interferometry.

Thermodiffusion of CO2 in Water by Nonequilibrium Molecular Dynamics Simulations

The components of a fluid mixture may segregate due to the Soret effect, a coupling phenomenon in which mass flux can be induced by a thermal gradient. In this work, we evaluate systematically the thermodiffusion of the CO₂-H₂O mixture, and the influence of the geothermal gradient on CO₂ segregation in deep saline aquifers in CO₂ storage. The eHeX method, a nonequilibrium molecular dynamics simulation approach, is judiciously selected to simulate the phenomenon. At 350 K, 400 bar, and CO₂ mole fraction of 0.02 (aquifer conditions), CO₂ accumulates on the cold side, and the thermal diffusion factor is close to 1 in a number of force fields. The lower the temperature, the higher is the separation and the thermal diffusion factor. In colder regions, water self-association is stronger, whereas the CO₂-H₂O cross-association and the CO₂-CO₂ interactions enhance at higher temperatures. Thermodiffusion and gravitational segregation have opposite effects on CO₂ segregation. At typical subsurface conditions, the Soret effect is more pronounced than gravity segregation, and CO₂ concentrates in the top (colder region). Our work sets the stage to model the effect of electrolytes on CO₂ segregation in subsurface aquifers and other areas of interest.

Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications

Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.

Insights into the mechanism of electrostatic field promoting ozone mass transfer in water: A molecular dynamics perspective

Ozone is the main role of ozone-based advanced oxidation process for organic wastewater treatment, which is usually added in water by aeration. However, the low solubility of ozone in water seriously affects the degradation efficiency. In this article, the external electrostatic field (EF) was proposed to improve the ozone solubility in water. The mass transfer characteristics of ozone in a gas-liquid two-phase system under EF were studied by molecular dynamics (MD) simulation. The microscopic mechanism of ozone mass transfer in water promoted by external EF was revealed by analyzing Gibbs dividing surface (GDS) interface structure, interfacial water molecular orientation, surface tension, liquid phase viscosity, hydrogen bond network and ozone self-diffusion coefficient. Our findings reveal that EF can enhance the thickness of GDS region (from 0.4648 nm to 0.4996 nm when EF is 0.2 V/nm) as well as its ozone content. The dipole moment orientation of water molecules also tends to point in the EF direction due to the influence of EF, making the difference in dipole moment orientation of water molecules in the first and second layers of GDS region gradually disappear. In addition, compared with the absence of EF, the existence of external EF can decrease the surface tension (from 77.6162 mN/m to 73.3480 mN/m when EF is 0.2 V/nm) at the gas-liquid interface and the viscosity of liquid phase (from 0.293 mP_a·s to 0.162 mP_a·s when EF is 0.2 V/nm), break the network of hydrogen bond in liquid phase, and increase the mobility of ozone (self-diffusion coefficient of ozone changes from 1.3232 × 10^-6 cm²·s^-1 to 1.8812 × 10^-6 cm²·s^-1 when EF is 0.2 V/nm). All these properties changes indicate that the presence of external EF enhances the ability of ozone to penetrate the interface of the two-phase system, and then improves the ozone mass transfer efficiency in water.

Hydrogen Bond Thermodynamics in Aqueous Acid Solutions: A Combined DFT and Classical Force-Field Approach

The thermodynamics of hydrogen bonds in aqueous and acidic solutions significantly impacts the kinetics and thermodynamics of acid reaction chemistry. We utilize in this work a multiscale approach, combining density functional theory (DFT) with classical molecular dynamics (MD) to model hydrogen bond thermodynamics in an acidic solution. Using thermodynamic cycles, we split the solution phase free energy into its gas phase counterpart plus solvation free energies. We validate this DFT/MD approach by calculating the aqueous phase hydrogen bond free energy between two water molecules (H₂O-···-H₂O), the free energy to transform an H₃O⁺ cation into an H₅O₂⁺ cation, and the hydrogen bond free energy of protonated water clusters (H₃O⁺-···-H₂O and H₅O₂⁺-···-H₂O). The computed equilibrium hydrogen bond free energy of H₂O-···-H₂O is remarkably accurate, especially considering the large individual contributions to the thermodynamic cycle. Turning to cations, we find the ion to be more stable than H₃O⁺ by roughly 1-2 k_BT. This small free energy difference allows for thermal fluctuation between the two idealized motifs, consistent with spectroscopic and simulation studies. Lastly, hydrogen bonding free energies between either H⁺ cation and H₂O in solution were found to be stronger than between two H₂O, though much less so than in vacuum because of dielectric screening in solution. Altogether, our results suggest the DFT/MD approach is promising for application in modeling hydrogen bonding and proton transfer thermodynamics in condensed phases.

Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model

For the past 50 years, researchers have sought molecular models that can accurately reproduce water's microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima near 223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ∼208 K. A local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is found to be the most probable hydrogen-bonding topology at all temperatures. This work suggests that MB-pol may provide predictive capability for studies of liquid water's physical properties across broad ranges of thermodynamic states, including the so-called water's "no man's land" which is difficult to probe experimentally.

Structure of benzothiadiazine at zwitterionic phospholipid cell membranes

The use of drugs derived from benzothiadiazine, which is a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension (treated with diuretics such as bendroflumethiazide or chlorothiazide), low blood sugar (treated with non-diuretic diazoxide), or the human immunodeficiency virus, among others. In this work, we have investigated the interactions of benzothiadiazine with the basic components of cell membranes and solvents, such as phospholipids, cholesterol, ions, and water. The analysis of the mutual microscopic interactions is of central importance to elucidate the local structure of benzothiadiazine as well as the mechanisms responsible for the access of benzothiadiazine to the interior of the cell. We have performed molecular dynamics simulations of benzothiadiazine embedded in three different model zwitterionic bilayer membranes made by dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine, and cholesterol inside aqueous sodium-chloride solution in order to systematically examine microscopic interactions of benzothiadiazine with the cell membrane at liquid-crystalline phase conditions. From data obtained through radial distribution functions, hydrogen-bonding lengths, and potentials of mean force based on reversible work calculations, we have observed that benzothiadiazine has a strong affinity to stay at the cell membrane interface although it can be fully solvated by water in short periods of time. Furthermore, benzothiadiazine is able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of different characteristic lengths.

Distinguishing Weak and Strong Hydrogen Bonds in Liquid Water-A Potential of Mean Force-Based Approach

The ability to form hydrogen bonds is one of the most important factors behind water's many anomalous properties. However, there is still no consensus on the hydrogen bond structure of liquid water, including the average number of hydrogen bonds in liquid water. We use molecular dynamics simulations of the polarizable iAMOEBA water model for investigating the hydrogen bond characteristics of liquid water over a wide range of temperatures and pressures. Geometric definitions of a hydrogen bond often use a rectangular region on the plane of hydrogen bond distances and angles. In this work, we find that an elliptical region is more appropriate for the identification of hydrogen bonds, based on statistically favorable molecular configurations. The two-dimensional potential of mean force (PMF) landscape along the hydrogen bond distance (O-H) and angle (O-H-O) is calculated for identifying the statistically favored molecular configurations, which is then used for defining hydrogen bond formation as well as the strength of a hydrogen bond. We further propose a new approach to characterize the hydrogen bonds as strong when the PMF is lower than -2 kT. Using this definition, a consistent explanation for the different average numbers of hydrogen bonds in water is obtained in agreement with the literature. Simulations are also performed with the rigid and nonpolarizable TIP4P/2005 water model. Both water models are qualitatively consistent in predicting the distribution of double-, single-, and non-donor configurations, in line with experimental data, while the iAMOEBA water model yields more quantitatively precise results, including a 10-15% double-donor fraction at 90 °C and 1 atm. The method is also demonstrated to be applicable to the recent, and more general, three-dimensional PMF-based definition of hydrogen bonds.

Two States of Water Converge to One State below 215 K

Anomalies of water have been explained by the two-state water model. In the model, water becomes one state upon supercooling. However, water crystallizes completely below 235 K ("no man's land"). The structural origin of the anomalous of the water is hidden in the "no man's land". To understand the properties of water, the spectroscopic experiment in "Norman's land" is inevitable. Hence, we proposed a new soft-confinement method for standard nuclear magnetic resonance spectroscopy to explore the "no man's land". We found the singularity temperature (215 K) at ambient pressure. Water exists in one state below 215 K. Above 215 K, the two states of water are supercritical states of the liquid-liquid critical point. The current study provides a perspective to determine the liquid-liquid critical point of water existing in a high-pressure condition.

Direct correlation of oxygen adsorption on platinum-electrolyte interfaces with the activity in the oxygen reduction reaction

The oxygen reduction reaction (ORR) on platinum catalysts is essential in fuel cells. Quantitative predictions of the relative ORR activity in experiments, in the range of 1 to 50 times, have remained challenging because of incomplete mechanistic understanding and lack of computational tools to account for the associated small differences in activation energies (<2.3 kilocalories per mole). Using highly accurate molecular dynamics (MD) simulation with the Interface force field (0.1 kilocalories per mole), we elucidated the mechanism of adsorption of molecular oxygen on regular and irregular platinum surfaces and nanostructures, followed by local density functional theory (DFT) calculations. The relative ORR activity is determined by oxygen access to platinum surfaces, which greatly depends on specific water adlayers, while electron transfer occurs at a similar slow rate. The MD methods facilitate quantitative predictions of relative ORR activities of any platinum nanostructures, are applicable to other catalysts, and enable effective MD/DFT approaches.

Electrostatic-modulated interfacial polymerization toward ultra-permselective nanofiltration membranes

Interfacial polymerization (IP) is a platform technology for ultrathin membranes. However, most efforts in regulating the IP process have been focused on short-range H-bond interaction, often leading to low-permselective membranes. Herein, we report an electrostatic-modulated interfacial polymerization (eIP) via supercharged phosphate-rich substrates toward ultra-permselective polyamide membranes. Phytate, a natural strongly charged organophosphate, confers high-density long-range electrostatic attraction to aqueous monomers and affords tunable charge density by flexible metal-organophosphate coordination. The electrostatic attraction spatially enriches amine monomers and temporally decelerates their diffusion into organic phase to be polymerized with acyl chloride monomers, triggering membrane sealing and inhibiting membrane growth, thus generating polyamide membranes with reduced thickness and enhanced cross-linking. The optimized nearly 10-nm-thick and highly cross-linked polyamide membrane displays superior water permeance and ionic selectivity. This eIP approach is applicable to the majority of conventional IP processes and can be extended to fabricate a variety of advanced membranes from polymers, supermolecules, and organic framework materials.

•

Electrostatic-modulated interfacial polymerization is proposed for the first time

•

Electrostatic attraction regulates the spatial-temporal distribution of amine monomers

•

Monomer regulation leads to reduced thickness and enhanced cross-linking of membrane

•

Ultrathin and highly cross-linked polyamide membrane displays superior permselectivity

Insights into the hydrogen bond network topology of phosphoric acid and water systems

Phosphoric acid and its mixtures with water are some of the best proton conducting materials known to science. Although the proton conductivity in pure phosphoric acid decreases upon external doping with excess H+ or OH-, the addition of water improves it substantially. A number of experimental and theoretical studies indicate that these systems form a very special case of hydrogen bond networks which not only facilitate fast proton transport but also show a number of other interesting properties such as glass forming ability. In this work, we present the molecular dynamics simulation results of the H3PO4-H2O system over the entire concentration range. The hydrogen bond networks were analyzed in terms of conventional microscopic as well as topological properties based on graph and network theory. The results show that the hydrogen bond network of H3PO4 is fundamentally different from that of H2O. On average, each phosphoric acid molecule tends to form more and stronger hydrogen bonds than water which leads to a much more connected and clustered network showing small-world properties which are absent in pure water. Moreover, these hydrogen bond network properties persist in the H3PO4-H2O mixtures as well, even at relatively high water contents. Finally, many of the physical properties such as molecular diffusion coefficients seem to be also intimately related to the network topological properties and follow similar trends with respect to system content. These results strongly indicate that many important properties such as proton transport in phosphoric acid and its aqueous systems are fundamentally related to their hydrogen bond network topology and might hold the key for their ultimate molecular understanding.

Born–Oppenheimer molecular dynamics simulations on structures of high-density and low-density water: a comparison of the SCAN meta-GGA and PBE GGA functionals

Using Born–Oppenheimer ab initio molecular dynamics (BOAIMD) simulations, the high-density water (HDW) and low-density water (LDW) structures based on SCAN meta-GGA are compared with those based on PBE GGA.

Computational study of the intermolecular interactions and their effect on the UV-visible spectra of the ternary liquid mixture of benzene, ethanol and propylene glycol

Quantum chemical calculations are well-equipped to provide answers to the questions regarding the different aspects of intermolecular interactions. We investigate the benzene, ethanol and 1,2 propanediol ternary mixture with theoretical as well as experimental UV-Vis spectroscopy. An extensive theoretical study on the molecular structure and UV-Vis spectral analysis was undertaken using density functional theory (DFT) method. Structural parameter analysis and the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) energy gap help to describe the possible interaction between molecules in dimer and in combination. Interaction energy has been calculated from topological study. Time-dependent density functional theory (TDDFT) calculations on dimer/cluster in gas phase help to understand the effect of the molecular interaction on the overall spectral shift and related intensity variation. Our results show that in the ternary mixture, the interaction energies of the interactions are π-π interaction: 0.52-2.57 kcal/mol, Hp-π interaction: 1.15 kcal/mol and H-bonding: 2.49 to 4.46 kcal/mol. The π-π interaction and H-bonding cause red shift in absorption spectra while Hp-π interaction causes blue shift. In the ternary mixture, the strength of different kinds of interaction depends on the concentration, and as each interaction has its own effect on spectral shift, the overall experimental spectra get broader and distorted from the Gaussian shape.

Unusually strong hydrogen bond cooperativity in particular (H2O)20 clusters

Drawing upon an intuitive charge-transfer-based picture of hydrogen bonding, we demonstrate that cooperativity effects acting in concert can lead to unusually strong hydrogen bonds in neutral water clusters. The structure, vibrational, and NMR properties of a (H2O)20 pentagonal dodecahedron cluster containing such a strong hydrogen bond were studied using second-order perturbation theory and density functional theory. The hydrogen bond length was found to be shorter than 2.50 Å. A large redshift of over 2000 cm-1 with respect to the isolated water molecule was predicted for the OH stretching frequency of the donor water molecule. A large downfield shift to 13.5 ppm of the isotropic part of the 1H magnetic shielding tensor together with an unusually large shielding anisotropy of 49.9 ppm was obtained. The hydrogen bond energy was calculated using symmetry-adapted perturbation theory and was found to be more than three times stronger than a typical hydrogen bond in liquid water.

Supercooled Low-Entropy Water Clusters

The properties of low-entropy water clusters and small bulk water domains in a hydrophobic solvent over a wide temperature range (235-333 K), including supercooling temperatures, were investigated. ¹H nuclear magnetic resonance spectroscopy showed singularity temperatures at ∼300, 250, 235, and 225 K. We proposed a model to understand these singularity temperatures in which the low-entropy water cluster is a locally favored tetrahedral structure (LFTS) and the small bulk water domain contains a mixture of disordered normal-liquid structure (DNLS) and LFTS. The model showed that the LFTS and DNLS populations change with applied temperature. Above ∼300 K, all local water structures become a DNLS. The population of LFTS increases with cooling and becomes dominant below ∼250 K. At ∼225 K, all local water structures converge to LFTS. The phase-transition rate of the low-entropy water clusters and small bulk water domains increases significantly at ∼235 K. The phase transition of the low-entropy water clusters showed primary ice nucleation. Low-entropy water clusters in a hydrophobic solvent are a unique water morphology and a probe material for water investigations.

Temperature Dependence of X-ray-Induced Auger Processes in Liquid Water

Auger spectroscopy has previously been used to study changes in the hydrogen bond network in liquid water, but to the best of our knowledge it has not been used to track such changes as a function of temperature. We show Auger spectroscopy to reflect the weakening of the hydrogen bond network upon heating. This shows that the radiation response of water, i.e., the relative propensity of the different processes occurring after radiation exposure, including femtosecond proton dynamics, depends on the temperature of the system. This proof-of-principle study further demonstrates the suitability of the technique to help elucidate information on the intermolecular structure of liquids such as water, opening the door to further temperature-dependent studies.

Rotational and Translational Diffusion of Proteins as a Function of Concentration

Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.

Binding and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes

The characterization of interactions between melatonin, one main ingredient of medicines regulating sleeping rhythms, and basic components of cellular plasma membranes (phospholipids, cholesterol, metal ions and water) is very important to elucidate the main mechanisms for the introduction of melatonin into cells and also to identify its local structure and microscopic dynamics. Molecular dynamics simulations of melatonin inside mixtures of dimyristoylphosphatidylcholine and cholesterol in NaCl solution at physiological concentration have been performed at 303.15 K to systematically explore melatonin-cholesterol, melatonin-lipid and melatonin-water interactions. Properties such as the area per lipid and thickness of the membrane as well as selected radial distribution functions, binding free energies, angular distributions, atomic spectral densities and translational diffusion of melatonin are reported. The presence of cholesterol significantly affects the behavior of melatonin, which is mainly buried into the interfaces of membranes. Introducing cholesterol into the system helps melatonin change from folded to extended configurations more easily. Our results suggest that there exists a competition between the binding of melatonin to phospholipids and to cholesterol by means of hydrogen-bonds. Spectral densities of melatonin reported in this work, in overall good agreement with experimental data, revealed the participation of each atom of melatonin to its complete spectrum. Melatonin self-diffusion coefficients are of the order of 10-7 cm2/s and they significantly increase when cholesterol is addeed to the membrane.

Insight into the antimicrobial mechanism of action of β2,2-amino acid derivatives from molecular dynamics simulation: Dancing the can-can at the membrane surface

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β^2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β^2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the "can-can pose". Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.

Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments

In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.

Inferences on hydrogen bond networks in water from isopermitive frequency investigations

Intermolecular hydrogen bonds play a crucial role in determining the unique characteristics of liquid water. We present low-frequency (1 Hz-40 MHz) dielectric spectroscopic investigations on water in the presence and absence of added solutes at different temperatures from 10 °C to 60 °C. The intersection points of temperature dependent permittivity contours at the vicinity of isopermitive frequency (IPF) in water are recorded and its properties are presumed to be related to the extent of hydrogen bond networks in water. IPF is defined as the frequency at which the relative permittivity of water is almost independent of temperature. The set of intersection points of temperature dependent permittivity contours at the vicinity of IPF are characterized by the mean [Formula: see text] and root-mean-square deviation/standard deviation [Formula: see text] associated with IPF. The tunability of M _IPF by the addition of NaCl and MgCl₂ salt emphasizes the strong correlation between the concentration of ions in water and the M _IPF. The [Formula: see text] is surmised to be related to the orientational correlations of water dipoles as well as to the intermolecular hydrogen bond networks in water. Further, alterations in [Formula: see text] is observed with the addition of kosmotropic and chaotropic solutes into water and are thought to arise due to the restructuring of hydrogen bond networks in water in presence of added solutes. Notably, the solute induced reconfiguration of hydrogen bond networks in water or often-discussed structure making/breaking effects of the added solutes in water can be inferred, albeit qualitatively, by examining the M _IPF and [Formula: see text]. Further, the Gaussian deconvoluted OH-stretching modes present in the Raman spectra of water and aqueous solutions of IPA and DMF strongly endorses the structural rearrangements occurring in water in presence of kosmotropes and chaotropes and are in line with the results derived from the root-mean-square deviation in IPF.

Diffusion and reaction pathways of water near fully hydrated TiO2 surfaces from ab initio molecular dynamics

Ab initio molecular dynamics simulations are reported for water-embedded TiO₂ surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO₂ surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO₂ which occur at full hydration, in addition to direct water splitting. Hydronium (H₃O⁺) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO₂ interfaces under ambient conditions.

Therapeutics for Inflammatory-Related Diseases Based on Plasmon-Activated Water: A Review

It is recognized that the properties of liquid water can be markedly different from those of bulk one when it is in contact with hydrophobic surfaces or is confined in nano-environments. Because our knowledge regarding water structure on the molecular level of dynamic equilibrium within a picosecond time scale is far from completeness all of water's conventionally known properties are based on inert "bulk liquid water" with a tetrahedral hydrogen-bonded structure. Actually, the strength of water's hydrogen bonds (HBs) decides its properties and activities. In this review, an innovative idea on preparation of metastable plasmon-activated water (PAW) with intrinsically reduced HBs, by letting deionized (DI) water flow through gold-supported nanoparticles (AuNPs) under resonant illumination at room temperature, is reported. Compared to DI water, the created stable PAW can scavenge free hydroxyl and 2,2-diphenyl-1-picrylhydrazyl radicals and effectively reduce NO release from lipopolysaccharide-induced inflammatory cells. Moreover, PAW can dramatically induce a major antioxidative Nrf2 gene in human gingival fibroblasts. This further confirms its cellular antioxidative and anti-inflammatory properties. In addition, innovatively therapeutic strategy of daily drinking PAW on inflammatory-related diseases based on animal disease models is demonstrated, examples being chronic kidney disease (CKD), chronic sleep deprivation (CSD), and lung cancer.

Estimating the energy of intramolecular hydrogen bonds from 1H NMR and QTAIM calculations

The values of the downfield chemical shift of the bridge hydrogen atom were estimated for a series of compounds containing an intramolecular hydrogen bond O-HO, O-HN, O-HHal, N-HO, N-HN, C-HO, C-HN and C-HHal. Based on these values, the empirical estimation of the hydrogen bond energy was obtained by using known relationships. For the compounds containing an intramolecular hydrogen bond, the DFT B3LYP/6-311++G(d,p) method was used both for geometry optimization and for QTAIM calculations of the topological parameters (electron density ρ^BCP and the density of potential energy V in the critical point of the hydrogen bond). The calculated geometric and topological parameters of hydrogen bonds were also used to evaluate the energy of the hydrogen bond based on the equations from the literature. Comparison of calibrating energies from the ¹H NMR data with the energies predicted by calculations showed that the most reliable are the linear dependence on the topological ρ^BCP and V parameters. However, the correct prediction of the hydrogen bond energy is determined by proper fitting of the linear regression coefficients. To obtain them, new linear relationships were found between the calculated ρ^BCP and V parameters and the hydrogen bond energies obtained from empirical ¹H NMR data. These relationships allow the comparison of the energies of different types of hydrogen bonds for various molecules and biological ensembles.

Solvent-induced stable pseudopolymorphism of Au(i)–thiolate lamellar assemblies: a model system for understanding the environment acclimation of biomacromolecules

Two pseudopolymorphs are achieved in two solvents and exhibit high structure preservation but have distinct optical properties, morphology and thermal stability.

Interaction between Water and Alkali Metal Ions and Its Temperature Dependence Revealed by Oxygen K-Edge X-ray Absorption Spectroscopy

Interaction between water molecules and alkali metal ions in aqueous salt solutions has been studied by the oxygen K-edge soft X-ray absorption spectroscopy (XAS) in transmission mode. In the measurement of several alkali halide aqueous solutions with different alkali chlorides (Li, Na, and K) and different sodium halides (Cl, Br, and I), the pre-edge component arising from the hydration water molecules shows a blue shift in peak energy as strongly depending on cations but not on anions. In the temperature dependent measurement, the pre-edge component arising from water molecules beyond the first hydration shell shows the same behavior as that of pure liquid water. On the other hand, the pre-edge component arising from water molecules in the first hydration shell of Li⁺ ions is not evidently dependent on the temperature, indicating that the hydration water molecules are more strongly bound with Li⁺ ions than the other water molecules. These experimental results are supported by the results of radial distribution functions of the first hydration shell and their temperature dependence, evaluated by molecular dynamics simulations.

Molecular dynamics simulation for the impact of an electrostatic field and impurity Mg2+ions on hard water

A detailed analysis of the structural parameters and dynamic parameters of hard water solutions under an external electrostatic field was performed by molecular dynamics (MD) simulations with the presence of impurity Mg²⁺ions.

Theoretical calculations of intramolecular hydrogen bond of the 2-Amino-2, 4, 6-cycloheptatrien-1-one in the gas phase and solution: Substituent effects and their positions

The density functional theory (DFT) method with 6-311[Formula: see text]G[Formula: see text] basis set has been used to calculate the intramolecular hydrogen bond, molecular structure, vibrational frequencies, nuclear quadrupole resonance (NQR) parameters, 1HNMR, and resonance parameters of 2-Amino-2, 4, 6-cycloheptatrien-1-one (2-amino tropone) and its 18 derivatives in 5 positions. The natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have been studied. The strongest and weakest hydrogen bonds exist for NO2 substituent in R3 position and OH in R7 position, respectively. In general, the substituted systems in position 3 indicate the stronger hydrogen bond in comparison with the parent molecule (R[Formula: see text]H), while, it is comparatively weaker for position 5. The energy of the N-H[Formula: see text]O interaction is found to be medium in strength ([Formula: see text][Formula: see text]kJ mol[Formula: see text] to [Formula: see text][Formula: see text]kJ mol[Formula: see text]). The low [Formula: see text], positive [Formula: see text] values and [Formula: see text] show that the nature of O [Formula: see text] H bonding is electrostatic. Also, our theoretical results show that the hydrogen bond strength in solution phase and the first singlet excited state is weaker in comparison with the gas phase ground state.

A Computational Study of the Protoisomerization of Indigo and Its Imine Derivatives

The protoisomerization (isomerization induced by protonation) mechanisms of indigo as well as indigo di- and monoimine derivatives were investigated using computational chemistry. Both density functional theory (M06-2X) and wave function theory (GMC-QDPT) methods were used to obtain reliable results. A solvation model (C-PCM with CH2Cl2 solvent) was employed to mimic the actual environment of the isomerization. The calculations reveal that the protoisomerizations of both the indigo and its imine derivatives are thermodynamically favorable. However, the energy barriers for rotating the double bonds in the derivatives are found to be lower than the one for indigo. More importantly, the imine derivatives undergo one-step isomerization, whereas a two-step process is predicted for indigo itself. The computational results provide insightful explanation for the different protoisomerization propensities of the parent indigo and its imine derivatives observed in experiment.

Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane

Understanding adaptation to extreme environments remains a challenge of high biotechnological potential for fundamental molecular biology. The cytosol of many microorganisms, isolated from saline environments, reversibly accumulates molar concentrations of the osmolyte ectoine to counterbalance fluctuating external salt concentrations. Although they have been studied extensively by thermodynamic and spectroscopic methods, direct experimental structural data have, so far, been lacking on ectoine-water-protein interactions. In this paper, in vivo deuterium labeling, small angle neutron scattering, neutron membrane diffraction and inelastic scattering are combined with neutron liquids diffraction to characterize the extreme ectoine-containing solvent and its effects on purple membrane of H. salinarum and E. coli maltose binding protein. The data reveal that ectoine is excluded from the hydration layer at the membrane surface and does not affect membrane molecular dynamics, and prove a previous hypothesis that ectoine is excluded from a monolayer of dense hydration water around the soluble protein. Neutron liquids diffraction to atomic resolution shows how ectoine enhances the remarkable properties of H-bonds in water—properties that are essential for the proper organization, stabilization and dynamics of biological structures.

How van der Waals interactions determine the unique properties of water

Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.